Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IAtomContainerSet.atomContainers()

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        if (shiftPasted) {
          double maxXCurr = Double.NEGATIVE_INFINITY;
            double minXPaste = Double.POSITIVE_INFINITY;

          for (IAtomContainer atc : moleculeSet.atomContainers()) {
              // Detect  the right border of the current structure..
              for (IAtom atom : atc.atoms()) {
                  if(atom.getPoint2d().x>maxXCurr)
                      maxXCurr = atom.getPoint2d().x;
              }
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        // in different reactions need separate layout (different positions etc)
        if (chemModel.getReactionSet() != null) {
            for (IReaction reaction : chemModel.getReactionSet().reactions()) {
                int i = 0;
                IAtomContainerSet products = reaction.getProducts();
                for (IAtomContainer product : products.atomContainers()) {
                    try {
                        products.replaceAtomContainer(i,
                                (IAtomContainer) product.clone());
                    } catch (CloneNotSupportedException e) {
                    }
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                    }
                    i++;
                }
                i = 0;
                IAtomContainerSet reactants = reaction.getReactants();
                for (IAtomContainer reactant : reactants.atomContainers()) {
                    try {
                        reactants.replaceAtomContainer(i,
                                (IAtomContainer) reactant.clone());
                    } catch (CloneNotSupportedException e) {
                    }
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        generateNewCoordinates(container);
      } else {
        // deal with disconnected atom containers
        IAtomContainerSet molecules = ConnectivityChecker
            .partitionIntoMolecules(container);
        for (IAtomContainer subContainer : molecules.atomContainers()) {
          generateNewCoordinates(subContainer);
        }
      }

      for (IAtom atom : container.atoms()) {
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        BufferedWriter out = new BufferedWriter(new FileWriter(outFile));

        String eol=System.getProperty("line.separator");
        if (object instanceof IChemModel) {
            IAtomContainerSet mSet = ((IChemModel) object).getMoleculeSet();
            for (IAtomContainer atc : mSet.atomContainers()) {
                InChI inchi = InChITool.generateInchi(atc);
                out.write(inchi.getInChI()+eol);
                out.write(inchi.getAuxInfo()+eol);
                out.write(inchi.getKey()+eol);
            }
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        //                       endPost < 0   endPost > 0
        //              ^                    ^
        //              |                    |
        //              --------------------->
        //
        for (IAtomContainer container : moleculeSet.atomContainers()) {
           
            // count the number of atoms before and after the arrow for this molecule
            int beforeStart = 0;
            int afterEnd = 0;
                      
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      reactantsorproducts = ReactionSetManipulator.getReactionByReactionID(chemModel.getReactionSet(), reactionID).getReactants();
    else
      reactantsorproducts = ReactionSetManipulator.getReactionByReactionID(chemModel.getReactionSet(), reactionID).getProducts();
    IReaction reaction = ReactionSetManipulator.getReactionByReactionID(chemModel.getReactionSet(), reactionID);
    int count=0;
    for(IAtomContainer mol : reactantsorproducts.atomContainers()){
      if(mol.getID().equals(movedContainer.getID())){
        reactantsorproducts.removeAtomContainer(count);
        break;
      }
      count++;
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